Commit 2c14d274 authored by Mathieu Giraud's avatar Mathieu Giraud

tools/affectanalyser.cpp: remove unused file

This was dead code, not working, with less features than ./vidjil -u
parent 20c60c19
#include <core/kmerstore.h>
#include <core/affectanalyser.h>
#include <core/fasta.h>
#include <core/read_chooser.h>
#include <core/read_score.h>
#include <iostream>
#include <fstream>
#include <cassert>
#include <string>
#include <cstdlib>
using namespace std;
int main(int argc, char **argv) {
int k = 14;
bool rc = true;
list<Sequence> sequences;
string input_file;
if ((argc > 1 && string(argv[1]) == "-h") || argc <= 3) {
cerr << "Usage: " << argv[0] << " repV repJ input_file" << endl;
exit(1);
}
Fasta seqV(argv[1]);
Fasta seqJ(argv[2]);
input_file = argv[3];
Fasta seq(input_file);
IKmerStore<KmerAffect> *index = new ArrayKmerStore<KmerAffect>(k, rc);
index->insert(seqV, "V");
index->insert(seqJ, "J");
for (int i=0; i < seq.size(); i++) {
AffectAnalyser<KmerAffect> *kaa = new KmerAffectAnalyser<KmerAffect>(*index, seq.sequence(i));
sequences.push_back(seq.read(i));
cout << seq.sequence(i) << endl;
cout << kaa->toString() << endl;
delete kaa;
}
VirtualReadScore *scorer = new KmerAffectReadScore(*index);
ReadChooser chooser(sequences, *scorer);
cout << "Best sequence is:" << endl << chooser.getBest() << endl;
delete scorer;
delete index;
cout << "Everything is ok!" << endl;
}
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